INSTALL.md

Prerequisites

1. System-Level Dependencies: Before using this tool, ensure the following are installed:
   • bedtools
   • Try::Tiny: Perl module that can be installed via CPAN

     sudo cpan install Try::Tiny
     

Not required, but depending on your system, might be needed: - pkg-config: May be required for building some Python libraries. - libmysqlclient-dev: May be required for mysqlclient. - build-essential: Provides gcc for compiling Python extensions. - Install these on Ubuntu/Debian: bash sudo apt update sudo apt install pkg-config libmysqlclient-dev build-essential

2. db.ini File:

   • Make a db.ini file and paste this (replacing <user> and <password> with your actual credentials):

     [postgresql]
     database=postgres
     host=<host>
     user=<user>
     password=<password>
     

3. Seven Bridges Credentials:

   • Set up credentials:

     mkdir -p ~/.sevenbridges
     vim ~/.sevenbridges/credentials

   • Paste this into the credentials file (replacing <token> with your actual token):

     [default]
     api_endpoint   = <api_endpoint>
     auth_token     = <token>
     advance_access = false
     

4. Seven Bridges Tools:

   • Install Seven Bridges CLI tools (not needed for ETL, but in case you want it installed):

     bash -c 'curl https://igor.sbgenomics.com/downloads/sb/install.sh -sSf | sudo -H sh'
     pip3 install pipx
     pipx ensurepath
     source ~/.bashrc
     pipx install sbpack

5. PedcBioPortal Access Token:

   • Required for running step 2.
   • File obtained from here, then clicking on Download Token. File is reusable until expired, then a new one will have to be downloaded.